nf-core/viralrecon report
Report generated on 2024-05-31, 11:19 PDT based on data in:
data/assemblydata/kraken2data/variantsdata/fastqc
nf-core/viralrecon summary
De novo assembly metrics
Summary of input reads, trimmed reads, and non-host reads. Generated by the nf-core/viralrecon pipeline
| Sample Name | # Input reads | # Trimmed reads (Cutadapt) | % Mapped reads | % Non-host reads (Kraken 2) | # SNPs | # SNPs | # Contigs | Largest contig | Genome fraction | N50 | Pangolin lineage | Nextclade clade |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SAMPLE1_PE | 55442 | 24125 | 99.5% | 100.0 | 7 | 1 | 1.0 | 29903.0 | 98.1% | 29903.0 | B.1 | 20A |
| SAMPLE2_PE | 42962 | 19160 | 98.9% | 99.8 | 7 | 1 | 1.0 | 29903.0 | 89.8% | 29903.0 | A.2 | 19B |
| SAMPLE3_SE | 49202 | 99.2% | 99.9 | 54 | 0 | 1.0 | 29903.0 | 97.4% | 29903.0 | B | 19A |
fastp
0.23.2
fastp An ultra-fast all-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...).DOI: 10.1093/bioinformatics/bty560.
Filtered Reads
Filtering statistics of sampled reads.
Insert Sizes
Insert size estimation of sampled reads.
Sequence Quality
Average sequencing quality over each base of all reads.
GC Content
Average GC content over each base of all reads.
N content
Average N content over each base of all reads.
Bcftools
1.16
Bcftools contains utilities for variant calling and manipulating VCFs and BCFs.DOI: 10.1093/gigascience/giab008.
Variant Substitution Types
Variant Quality
Indel Distribution
Variant depths
Read depth support distribution for called variants
Bowtie 2 / HiSAT2
Bowtie 2 and HISAT2 are fast and memory-efficient tools for aligning sequencing reads against a reference genome. Unfortunately both tools have identical log output by default, so it is impossible to distiguish which tool was used. .DOI: 10.1038/nmeth.1923; 10.1038/nmeth.3317; 10.1038/s41587-019-0201-4.
Single-end alignments
This plot shows the number of reads aligning to the reference in different ways.
There are 3 possible types of alignment:
- SE mapped uniquely: Read has only one occurence in the reference genome.
- SE multimapped: Read has multiple occurence.
- SE not aligned: Read has no occurence.
Paired-end alignments
This plot shows the number of reads aligning to the reference in different ways.
There are 6 possible types of alignment:
- PE mapped uniquely: Pair has only one occurence in the reference genome.
- PE mapped discordantly uniquely: Pair has only one occurence but not in proper pair.
- PE one mate mapped uniquely: One read of a pair has one occurence.
- PE multimapped: Pair has multiple occurence.
- PE one mate multimapped: One read of a pair has multiple occurence.
- PE neither mate aligned: Pair has no occurence.
Cutadapt
4.2
Cutadapt is a tool to find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.DOI: 10.14806/ej.17.1.200.
Filtered Reads
This plot shows the number of reads (SE) / pairs (PE) removed by Cutadapt.
Trimmed Sequence Lengths
This plot shows the number of reads with certain lengths of adapter trimmed.
Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak may be related to adapter length.
See the cutadapt documentation for more information on how these numbers are generated.
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).